Contacts of the helix formed by residues 92 - 100 (chain D) in PDB entry 2OX6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 92 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR 3.3 1.1 + - - +
91D PRO* 1.3 87.6 - - + +
93D GLN* 1.3 64.9 + - - +
94D ALA* 3.6 8.9 + - - +
95D ILE* 3.1 34.8 + - + +
96D TYR* 2.9 23.6 + - - +
110D THR* 4.0 6.7 - - - -
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Residues in contact with GLN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D THR* 1.3 72.5 - - - +
94D ALA* 1.3 61.9 + - - +
96D TYR* 3.3 5.3 + - - +
97D THR* 3.0 51.2 + - + +
104D LEU* 4.6 0.2 - - - +
108D PRO 2.8 24.8 + - - -
109D LEU* 3.4 19.1 - - + +
110D THR* 2.9 35.5 + - + +
111D GLU* 4.5 1.7 - - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR* 3.3 9.7 + - - +
93D GLN* 1.3 76.8 - - - +
95D ILE* 1.3 61.3 + - + +
97D THR* 2.7 21.6 + - - -
98D GLN* 3.1 29.1 - - - +
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR* 3.9 18.6 - - + -
91D PRO* 4.0 31.4 - - + -
92D THR* 3.1 29.1 + - + +
94D ALA* 1.3 75.1 - - + +
96D TYR* 1.3 67.1 + - - +
98D GLN* 3.2 11.6 + - - +
99D TYR* 3.1 28.7 + - + +
137D LEU* 4.1 18.4 - - + +
139D VAL* 4.0 23.3 - - + +
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Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR* 3.6 15.4 - + + +
92D THR 2.9 16.4 + - - +
93D GLN* 3.3 9.2 + - - +
95D ILE* 1.3 78.2 - - - +
97D THR* 1.3 54.7 + - - +
100D ASN* 2.8 66.5 + - + +
103D PHE* 3.6 14.3 - - + +
104D LEU* 3.9 18.6 - - + -
107D LEU* 2.5 41.9 + - - +
108D PRO 4.0 0.9 - - - -
109D LEU 3.6 12.8 - - - -
110D THR* 3.5 33.0 - - - +
113D TYR* 3.4 33.2 - + + +
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Residues in contact with THR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLN* 3.0 39.4 + - + +
94D ALA* 2.7 24.6 + - - -
96D TYR* 1.3 75.9 - - + +
98D GLN* 1.3 63.1 + - - +
99D TYR 3.5 0.2 + - - -
100D ASN 3.9 4.6 + - - +
101D PRO* 4.2 10.9 - - - +
104D LEU* 3.6 34.8 - - + +
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Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA* 3.1 30.3 + - - +
95D ILE* 3.6 11.5 - - - +
97D THR* 1.3 86.3 + - - +
99D TYR* 1.3 81.6 + - + +
101D PRO* 4.2 6.4 - - - +
139D VAL* 5.4 3.1 - - - +
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Residues in contact with TYR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D TYR* 3.6 22.2 - - + -
95D ILE* 3.1 19.4 + - + +
98D GLN* 1.3 97.9 + - + +
100D ASN* 1.3 58.8 + - - +
101D PRO* 3.4 9.4 - - - +
102D GLU* 4.4 0.5 - - - +
137D LEU* 3.8 18.6 - - + -
139D VAL* 3.6 36.9 - - + +
142D TYR* 4.1 15.3 - + - -
143D LYS* 3.8 14.0 + - - +
146D ARG* 5.5 2.1 + - - -
153D GLU* 3.6 35.7 - - + -
155D ARG* 3.7 3.1 + - - -
158D ARG* 2.9 38.3 + - - +
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Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TYR* 3.3 38.0 - - - -
96D TYR* 2.8 46.9 + - + +
97D THR 4.3 2.9 - - - -
98D GLN 3.7 0.4 - - - -
99D TYR* 1.3 77.1 - - - +
101D PRO* 1.3 65.9 - - - +
102D GLU 3.2 2.7 - - - -
103D PHE* 3.2 19.4 + - + -
104D LEU* 3.2 15.2 + - - +
113D TYR* 4.3 2.9 - - - -
155D ARG* 2.5 38.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il